removeZeros: Remove Zeros

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Remove Zeros

Description

Remove Zeros

Usage

removeZeros(x)

Arguments

x	A phyloseq object or a data.frame with only numerical or matrix

Details

In phyloseq based analysis, prune_samples or subset_samples does not remove taxa that have zero abundances in remaining samples. In such cases user may want to exclude these taxa.

Value

If input is phyloseq, returns phyloseq with taxa that have zeros in all samples. If input is matrix or data frame, returned object is without rows and cloumns that sum to zero.

Author(s)

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
ps1 <- subset_samples(FuentesIliGutData, ILI != "L2")
ps1
ps2 <- removeZeros(ps1)
ps2

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.